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- PDB-3fvz: Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) -

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Basic information

Entry
Database: PDB / ID: 3fvz
TitleStructure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL)
ComponentsPeptidyl-glycine alpha-amidating monooxygenase
KeywordsLYASE / BETA PROPELLER / PEPTIDE AMIDATION / HG-MAD / ZN-MAD / Cleavage on pair of basic residues / Cytoplasmic vesicle / Glycoprotein / Membrane / Metal-binding / Monooxygenase / Multifunctional enzyme / Oxidoreductase / Phosphoprotein / Sulfation / Transmembrane / Vitamin C
Function / homology
Function and homology information


peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process ...peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process / mitotic chromosome condensation / response to pH / L-ascorbic acid binding / response to copper ion / limb development / response to zinc ion / transport vesicle membrane / maternal process involved in female pregnancy / response to glucocorticoid / condensed chromosome / lactation / secretory granule / regulation of actin cytoskeleton organization / trans-Golgi network / response to estradiol / heart development / perikaryon / response to hypoxia / response to xenobiotic stimulus / copper ion binding / neuronal cell body / calcium ion binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / cell surface / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. ...Peptidylglycine alpha-hydroxylating monooxygenase/peptidyl-hydroxyglycine alpha-amidating lyase / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / Peptidylglycine alpha-amidating monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsChufan, E.E. / De, M. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
CitationJournal: Structure / Year: 2009
Title: Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.
Authors: Chufan, E.E. / De, M. / Eipper, B.A. / Mains, R.E. / Amzel, L.M.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-glycine alpha-amidating monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3197
Polymers36,9141
Non-polymers4056
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.176, 75.056, 97.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-glycine alpha-amidating monooxygenase / PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha- ...PAM / Peptidylglycine alpha-hydroxylating monooxygenase / PHM / Peptidyl-alpha-hydroxyglycine alpha-amidating lyase / Peptidylamidoglycolate lyase / PAL


Mass: 36914.090 Da / Num. of mol.: 1
Fragment: Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase catalytic core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Cell line (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14925, peptidylamidoglycolate lyase

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Non-polymers , 6 types, 154 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate pH=4.8, 0.2mM zinc(II) acetate, 0.2mM iron(III) chloride - 0.2ml mother liquor in reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.28241 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 18, 2007
RadiationMonochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28241 Å / Relative weight: 1
ReflectionResolution: 2.35→39.22 Å / Num. all: 16524 / Num. obs: 16524 / % possible obs: 99.7 % / Redundancy: 11.3 % / Rsym value: 0.06 / Net I/σ(I): 60.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1560 / Rsym value: 0.49 / % possible all: 96.9

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.35→39.22 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.593 / SU ML: 0.199 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26333 847 5.1 %RANDOM
Rwork0.20321 ---
obs0.20615 15620 99.63 %-
all-16524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.026 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--3.19 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 19 148 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212829
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9223853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68624.15147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1815432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3751513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022260
X-RAY DIFFRACTIONr_nbd_refined0.1930.21247
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21794
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.29
X-RAY DIFFRACTIONr_mcbond_it0.3281.51755
X-RAY DIFFRACTIONr_mcangle_it0.56222783
X-RAY DIFFRACTIONr_scbond_it0.77331201
X-RAY DIFFRACTIONr_scangle_it1.1124.51070
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 73 -
Rwork0.254 1071 -
obs-1560 95.65 %

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